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Wednesday, January 13, 2016

They discuss trying to get to shapes with meaning. Can a scribble on a
page mutate to a han character with meaning? (protein folds)

“mutations and natural selection have limits and they can’t innovate
anything unless the function they are innovating is already present…
you already have to have the designed feature there in order to get it
to improve… you cannot improve a pigment cell to an eye unless you
already have something like an eye there.”

Since biological inventions only benefit their possessors after they
work, their origins cannot be attributed to their selective effects. One
proposed solution to this conundrum is that selection perfects
activities that already existed in rudimentary form before they became
beneficial. An example of this idea for protein origins is the
promiscuity hypothesis, which claims that minor aberrant side-reactions
in enzymes can be evolutionary starting points for proficient new
enzymes. Another example—the junk hypothesis—claims that proteins
arising from accidental expression of non-genic DNA may likewise have
slight activities that, through evolutionary optimization, lead to
proficient enzymes. Here, we tested these proposals by observing how the
endpoint of simple evolutionary optimization depends on the starting
point. Beginning with optimization of protein-like constructs in the
Stylus computational model, we compared promiscuous and junk starting
points, where design elements specific to the test function were
completely absent, to a starting point that retained most elements of a
good design (mutation having disrupted some). In all three cases,
evolutionary optimization improved activities by a large factor. The
extreme weakness of the original activities, however, meant even large
improvements could be inconsequential. Indeed, the endpoint was itself a
proficient design only in the case where this design was largely
present from the outset. Laboratory optimization of
ampicillin-resistance proteins derived from a natural beta lactamase
produced similar results. Our junk protein here was a deletion mutant
that somehow confers weak resistance without the original catalytic
mechanism (much of the active site having been lost). Evolutionary
optimization was unable to improve that mutant. In contrast, a
comparably weak mutant that retained the active site surpassed the
natural beta lactamase after six rounds of selection. So, while mutation
and selection can improve the proficiency of good designs through small
structural adjustments, they seem unable to convert fortuitous
selectable activities into good designs. http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2015.2